Introduction | Summary of features | Fitting a model | The discrete gamma-GPD spliced threshold model | The Type-I Pareto model | Density, distribution, and quantile functions, plus simulating data | Doing comparative analysis | Extracting diversity estimators | Bootstrapping model fits | References
Package: powerTCR 1.33.0
Hillary Koch
powerTCR: Model-Based Comparative Analysis of the TCR Repertoire
This package provides a model for the clone size distribution of the TCR repertoire. Further, it permits comparative analysis of TCR repertoire libraries based on theoretical model fits.
Authors:
powerTCR_1.33.0.tar.gz
powerTCR_1.33.0.zip(r-4.7)powerTCR_1.33.0.zip(r-4.6)powerTCR_1.33.0.zip(r-4.5)
powerTCR_1.33.0.tgz(r-4.6-any)powerTCR_1.33.0.tgz(r-4.5-any)
powerTCR_1.33.0.tar.gz(r-4.7-any)powerTCR_1.33.0.tar.gz(r-4.6-any)
powerTCR_1.33.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
powerTCR/json (API)
| # Install 'powerTCR' in R: |
| install.packages('powerTCR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- repertoires - Two toy examples of sample TCR repertoires.
On BioConductor:powerTCR-1.33.0(bioc 3.24)powerTCR-1.32.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
softwareclusteringbiomedicalinformatics
Last updated from:5c4d0f2395. Checks:1 ERROR, 7 WARNING, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 167 | ||
| linux-devel-x86_64 | WARNING | 257 | ||
| source / vignettes | OK | 184 | ||
| linux-release-x86_64 | WARNING | 241 | ||
| macos-release-arm64 | WARNING | 114 | ||
| macos-oldrel-arm64 | WARNING | 101 | ||
| windows-devel | WARNING | 128 | ||
| windows-release | WARNING | 125 | ||
| windows-oldrel | WARNING | 119 | ||
| wasm-release | OK | 114 |
Exports:clusterPlotddiscgammagpdfdespondsfdiscgammagpdget_bootstrapsget_distancesget_diversityget_mleget_nllhJS_despondsJS_distJS_splicedpdiscgammagpdqdiscgammagpdrdiscgammagpd
Dependencies:cliclustercodetoolscubaturedoParallelevdevmixforeachgluegsliteratorslatticelifecyclemagrittrMASSMatrixmgcvnlmepermutepurrrRcpprlangSparseMtruncdistvctrsveganVGAM
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Grab important output from a list of fits | get_diversity get_mle get_nllh |
| Visualize hierarchical clustering of samples | clusterPlot |
| The discrete gamma-GPD spliced threshold distribution | ddiscgammagpd pdiscgammagpd qdiscgammagpd rdiscgammagpd |
| Fit the type-I Pareto distribution as according to Desponds et al. (2016) | fdesponds |
| Fit the discrete gamma-GPD spliced threshold model | fdiscgammagpd |
| Get bootstrapped fits for a list of fitted models | get_bootstraps |
| Compute matrix of pairwise Jensen-Shannon Distances | get_distances |
| Compute the Jensen-Shannon distance between two fitted distributions using the Desponds model | JS_desponds |
| Compute the Jensen-Shannon distance between two model fits | JS_dist |
| Compute the Jensen-Shannon distance between two fitted discrete gamma-GPD spliced threshold distributions | JS_spliced |
| Load in and parse TCR data files for use by powerTCR | parseFile parseFolder |
| Two toy examples of sample TCR repertoires. | repertoires |
